Differentially abundant species
Silvia Raineri
09/10/2020
Analysis of Differentially Abundant species
This is an analysis of differentially abundant species in obese rats upon treatment long-term (42 Days) treatment with Sibutramine. To achieve this, DESeq2 was used with the model: ~ number + day
## Number significant = 192Plot Boxplots for all differentially abundant species
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## [1] 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
## [1] 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
## [1] 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80
## [1] 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
## [20] 100
## [1] 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
## [20] 120
## [1] 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
## [20] 140
## [1] 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
## [20] 160
## [1] 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
## [20] 180
# Focus on Bacteroides species Below a focus on all the differentially abundant Bacteroides species
Ratio Bacteroidetes/Firmicutes
Below are the details of the R session that was used when this script was executed.
## R version 3.6.1 (2019-07-05)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Mojave 10.14.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] DESeq2_1.24.0 SummarizedExperiment_1.14.1
## [3] DelayedArray_0.10.0 BiocParallel_1.18.1
## [5] matrixStats_0.56.0 Biobase_2.44.0
## [7] GenomicRanges_1.36.1 GenomeInfoDb_1.20.0
## [9] IRanges_2.18.3 S4Vectors_0.22.1
## [11] BiocGenerics_0.30.0 reshape2_1.4.4
## [13] ggrepel_0.8.2 vegan_2.5-6
## [15] lattice_0.20-41 permute_0.9-5
## [17] phyloseq_1.28.0 ggpubr_0.4.0
## [19] forcats_0.5.0 stringr_1.4.0
## [21] dplyr_1.0.2 purrr_0.3.4
## [23] readr_1.3.1 tidyr_1.1.2
## [25] tibble_3.0.3 ggplot2_3.3.2
## [27] tidyverse_1.3.0
##
## loaded via a namespace (and not attached):
## [1] readxl_1.3.1 backports_1.1.9 Hmisc_4.4-1
## [4] plyr_1.8.6 igraph_1.2.5 splines_3.6.1
## [7] digest_0.6.25 foreach_1.5.0 htmltools_0.5.0
## [10] fansi_0.4.1 magrittr_1.5 checkmate_2.0.0
## [13] memoise_1.1.0 cluster_2.1.0 openxlsx_4.1.5
## [16] Biostrings_2.52.0 annotate_1.62.0 modelr_0.1.8
## [19] jpeg_0.1-8.1 colorspace_1.4-1 blob_1.2.1
## [22] rvest_0.3.6 haven_2.3.1 xfun_0.16
## [25] crayon_1.3.4 RCurl_1.98-1.2 jsonlite_1.7.0
## [28] genefilter_1.66.0 survival_3.2-3 iterators_1.0.12
## [31] ape_5.4-1 glue_1.4.2 gtable_0.3.0
## [34] zlibbioc_1.30.0 XVector_0.24.0 car_3.0-9
## [37] Rhdf5lib_1.6.3 abind_1.4-5 scales_1.1.1
## [40] DBI_1.1.0 rstatix_0.6.0 Rcpp_1.0.5
## [43] xtable_1.8-4 htmlTable_2.0.1 foreign_0.8-76
## [46] bit_4.0.4 Formula_1.2-3 htmlwidgets_1.5.1
## [49] httr_1.4.2 RColorBrewer_1.1-2 ellipsis_0.3.1
## [52] farver_2.0.3 pkgconfig_2.0.3 XML_3.99-0.3
## [55] nnet_7.3-14 dbplyr_1.4.4 locfit_1.5-9.4
## [58] labeling_0.3 tidyselect_1.1.0 rlang_0.4.7
## [61] AnnotationDbi_1.46.1 munsell_0.5.0 cellranger_1.1.0
## [64] tools_3.6.1 cli_2.0.2 generics_0.0.2
## [67] RSQLite_2.2.0 ade4_1.7-15 broom_0.7.0
## [70] evaluate_0.14 biomformat_1.12.0 yaml_2.2.1
## [73] knitr_1.29 bit64_4.0.5 fs_1.5.0
## [76] zip_2.1.1 nlme_3.1-149 xml2_1.3.2
## [79] compiler_3.6.1 rstudioapi_0.11 curl_4.3
## [82] png_0.1-7 ggsignif_0.6.0 reprex_0.3.0
## [85] geneplotter_1.62.0 stringi_1.4.6 Matrix_1.2-18
## [88] multtest_2.40.0 vctrs_0.3.4 pillar_1.4.6
## [91] lifecycle_0.2.0 cowplot_1.0.0 data.table_1.12.8
## [94] bitops_1.0-6 R6_2.4.1 latticeExtra_0.6-29
## [97] gridExtra_2.3 rio_0.5.16 codetools_0.2-16
## [100] MASS_7.3-52 assertthat_0.2.1 rhdf5_2.28.1
## [103] withr_2.2.0 GenomeInfoDbData_1.2.1 mgcv_1.8-33
## [106] hms_0.5.3 grid_3.6.1 rpart_4.1-15
## [109] rmarkdown_2.3 carData_3.0-4 lubridate_1.7.9
## [112] base64enc_0.1-3